Dcoef-methods: Dcoef
In snjy9182/smt-beta: Statistical analysis of single molecule trajectories

Description Usage Arguments Details Value Examples

Caclulate diffusion coefficient (Dcoef) for trajecotries.

Dcoef( MSD=NULL,trackll=NULL,dt=6,filter=c(min=7,max=Inf),rsquare=0.8,
       resolution=0.107,binwidth=NULL,method=c("static","percentage",
       "rolling.window"),plot=FALSE,output=FALSE,t.interval=0.01,
       profile=NULL)

`MSD`	Mean Square Displacement calculated using msd() function. Either MSD or trackll can be passed into Dcoef for calculation of diffusion coefficient.
`trackll`	Track list output from readDiatrack().
`dt`	Time intervals. Default 6.
`filter`	a vector specifies the minimum and max length of trajecotries to be analyzed. Take only trajectories that has number of frames greater than (>=) min and less than (<) max.
`rsquare`	rsquare filter on Dcoef results. Default to be 0.8. Set value to 0 if rsquare filter is not desired.
`resolution`	ratio of pixel to uM.
`binwidth`	binwidth used for histogram. Default NULL, automatically assign binwidth.
`method`	"static", uses time lags 2~5 to calculate diffusion coefficient; "percentage", uses (tierd) percentage (default 0.25) of time lags (see Details). "rolling.window", time lags uses for Dcoef follows a rolling window with specified window size (default 4).
`plot`	A parameter for plotting. Default FALSE, no plot; If TRUE, automatically plots 'histogram' with count information, binwidth can be set through parameter binwidth; as well as 'density' with density/frequency.
`output`	An Logical indicate if output should be generated. See Values for detail.
`t.interval`	time interval between frames, default 0.010 s (10ms).
`profile`	Location of preference file. By default (NULL), it is stored at : system.file("extdata","PREF","profile.csv",package="sojourner"). User can provide preference file by specifying the location of the file, e.g. profile="/Users/shengliu/Desktop/profile.csv".

Generic parameters (parameter applied to all methods, such as resolution etc) are set in the function. Method dependent parameters (such as lag.start, lag.end for method = "static"), are stored in profile.csv in PREF folder under extdata. To change preference parameter, can either programably or manually go to folder system.file("extdata","PREF","profile.csv",package="sojourner"), and c hange the profile.csv.

lag.start: time lag used as start of dt for compute Dcoef. Default 2.

lag.end: Time lag used as end of dt for compute Dcoef. Default 2.

method for calculating Dcoef:

static stabilize the number of time lags used for fitting using time lag 2~ 5 despite the total time lags measured.

percentage "percentage", uses (tierd) percentage (default 0.25) of time lags.

[,1]	TrackLength	Percentage	TimeLagsForFitting
[,2]	31~	0.25	2~5-2~7
[,3]	22~30	0.25	2~5-2~7
[,4]	15~21	0.4	2~5-2~7
[,5]	10~15	0.6	2~5-2~7
[,6]	7~9	1	2~5-2~7

rolling.window time lags uses for Dcoef follows a rolling window with specified window size (default 4).

Dcoef A list of Dcoef for each file in trackll.
PDF Log.Dcoef histogram fitted with density curve, when plot = TRUE.
csv Dcoef output in csv format, when output = TRUE.

# compare files
folder=system.file("extdata",'SWR1',package="sojourner")
trackll = createTrackll(folder=folder, input=3)
MSD=msd(trackll=trackll)
Dcoef(MSD=MSD,method="static",plot=TRUE)

# compare folders
folder1=system.file("extdata",'SWR1',package="sojourner")
folder2=system.file("extdata",'HTZ1',package="sojourner")
trackll2=compareFolder(folders=c(folder1,folder2), input=3)
Dcoef(trackll=trackll2,method="percentage",plot=TRUE)
Dcoef(trackll=trackll2,method="rolling.window",plot=TRUE)